[R-pkg-team] Bug#1126236: r-cran-phylobase: FTBFS: ERROR: lazy loading failed for package 'phylobase'

[Santiago Vila]

Package: src:r-cran-phylobase
Version: 0.8.12-2
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, this package failed to build.

Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:

https://people.debian.org/~sanvila/build-logs/202601/

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:r-cran-phylobase, so that this is still
visible in the BTS web page for this package.

Thanks.

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[...]
 debian/rules clean
dh clean --buildsystem R
   dh_auto_clean -O--buildsystem=R
   dh_autoreconf_clean -O--buildsystem=R
   dh_clean -O--buildsystem=R
 debian/rules binary
dh binary --buildsystem R
   dh_update_autotools_config -O--buildsystem=R
   dh_autoreconf -O--buildsystem=R
   dh_auto_configure -O--buildsystem=R
   dh_auto_build -O--buildsystem=R
   dh_auto_test -O--buildsystem=R
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--buildsystem=R
   dh_prep -O--buildsystem=R
   dh_auto_install --destdir=debian/r-cran-phylobase/ -O--buildsystem=R
I: R packages needed for DEP8: mass, testthat (>= 0.8.1), knitr, rmarkdown
I: R Package: phylobase Version: 0.8.12
I: Building using R version 4.5.2-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Fri, 26 Dec 2025 17:10:48 +0900
	mkdir -p /<<PKGBUILDDIR>>/debian/r-cran-phylobase/usr/lib/R/site-library
	R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-cran-phylobase/usr/lib/R/site-library --clean . --built-timestamp="'Fri, 26 Dec 2025 17:10:48 +0900'"
* installing *source* package ‘phylobase’ ...
** this is package ‘phylobase’ version ‘0.8.12’
** package ‘phylobase’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Debian 15.2.0-12) 15.2.0’
using C++ compiler: ‘g++ (Debian 15.2.0-12) 15.2.0’
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/usr/lib/R/site-library/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.5.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2   -c RcppExports.cpp -o RcppExports.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/usr/lib/R/site-library/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.5.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c ancestors.c -o ancestors.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/usr/lib/R/site-library/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.5.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2   -c checkPhylo4.cpp -o checkPhylo4.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/usr/lib/R/site-library/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.5.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c descendants.c -o descendants.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/usr/lib/R/site-library/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.5.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c phyloXX.c -o phyloXX.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/usr/lib/R/site-library/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.5.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c phylobase_init.c -o phylobase_init.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/usr/lib/R/site-library/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.5.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c reorderBinary.c -o reorderBinary.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/usr/lib/R/site-library/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.5.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c reorderRobust.c -o reorderRobust.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o phylobase.so RcppExports.o ancestors.o checkPhylo4.o descendants.o phyloXX.o phylobase_init.o reorderBinary.o reorderRobust.o -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
installing to /<<PKGBUILDDIR>>/debian/r-cran-phylobase/usr/lib/R/site-library/00LOCK-r-cran-phylobase-0.8.12/00new/phylobase/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘loadRcppModules’ is not exported by 'namespace:Rcpp'
Execution halted
ERROR: lazy loading failed for package ‘phylobase’
* removing ‘/<<PKGBUILDDIR>>/debian/r-cran-phylobase/usr/lib/R/site-library/phylobase’
dh_auto_install: error: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-cran-phylobase/usr/lib/R/site-library --clean . --built-timestamp="'Fri, 26 Dec 2025 17:10:48 +0900'" returned exit code 1
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
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